Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-...

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Autores: Bickhart, Derek M., Xu, Lingyang, Hutchison, Jana L., Cole, John B., Null, Daniel J., Schroeder, Steven G., Song, Jiuzhou, Garcia, Jose Fernando [UNESP], Sonstegard, Tad S., Van Tassell, Curtis P., Schnabel, Robert D., Taylor, Jeremy F., Lewin, Harris A., Liu, George E.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:Brasil
Institución:Universidade Estadual Paulista (UNESP)
Repositorio:Repositório Institucional da UNESP
Idioma:inglés
OAI Identifier:oai:repositorio.unesp.br:11449/178113
Acceso en línea:http://dx.doi.org/10.1093/dnares/dsw013
http://hdl.handle.net/11449/178113
Access Level:acceso abierto
Palabra clave:cattle genome
copy number variation
indicine
population sequencing
taurine
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spelling Diversity and population-genetic properties of copy number variations and multicopy genes in cattlecattle genomecopy number variationindicinepopulation sequencingtaurineThe diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future.USDA-ARS Animal Genomics and Improvement LaboratoryDepartment of Animal and Avian Sciences University of MarylandUniversidade Estadual Paulista (UNESP)Division of Animal Sciences University of MissouriInformatics Institute University of MissouriDepartment of Evolution and Ecology University of CaliforniaUniversidade Estadual Paulista (UNESP)Animal Genomics and Improvement LaboratoryUniversity of MarylandUniversidade Estadual Paulista (Unesp)University of MissouriUniversity of California2018-12-11T17:28:48Z2018-12-11T17:28:48Z2016-06-15info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article253-262application/pdfhttp://dx.doi.org/10.1093/dnares/dsw013DNA Research, v. 23, n. 3, p. 253-262, 2016.1756-16631340-2838http://hdl.handle.net/11449/17811310.1093/dnares/dsw0132-s2.0-849763636052-s2.0-84976363605.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengDNA Research2,866info:eu-repo/semantics/openAccessBickhart, Derek M.Xu, LingyangHutchison, Jana L.Cole, John B.Null, Daniel J.Schroeder, Steven G.Song, JiuzhouGarcia, Jose Fernando [UNESP]Sonstegard, Tad S.Van Tassell, Curtis P.Schnabel, Robert D.Taylor, Jeremy F.Lewin, Harris A.Liu, George E.2025-06-07T05:09:15Zoai:repositorio.unesp.br:11449/178113Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestrepositoriounesp@unesp.bropendoar:29462025-06-07T05:09:15Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Diversity and population-genetic properties of copy number variations and multicopy genes in cattle
title Diversity and population-genetic properties of copy number variations and multicopy genes in cattle
spellingShingle Diversity and population-genetic properties of copy number variations and multicopy genes in cattle
Bickhart, Derek M.
cattle genome
copy number variation
indicine
population sequencing
taurine
title_short Diversity and population-genetic properties of copy number variations and multicopy genes in cattle
title_full Diversity and population-genetic properties of copy number variations and multicopy genes in cattle
title_fullStr Diversity and population-genetic properties of copy number variations and multicopy genes in cattle
title_full_unstemmed Diversity and population-genetic properties of copy number variations and multicopy genes in cattle
title_sort Diversity and population-genetic properties of copy number variations and multicopy genes in cattle
dc.creator.none.fl_str_mv Bickhart, Derek M.
Xu, Lingyang
Hutchison, Jana L.
Cole, John B.
Null, Daniel J.
Schroeder, Steven G.
Song, Jiuzhou
Garcia, Jose Fernando [UNESP]
Sonstegard, Tad S.
Van Tassell, Curtis P.
Schnabel, Robert D.
Taylor, Jeremy F.
Lewin, Harris A.
Liu, George E.
author Bickhart, Derek M.
author_facet Bickhart, Derek M.
Xu, Lingyang
Hutchison, Jana L.
Cole, John B.
Null, Daniel J.
Schroeder, Steven G.
Song, Jiuzhou
Garcia, Jose Fernando [UNESP]
Sonstegard, Tad S.
Van Tassell, Curtis P.
Schnabel, Robert D.
Taylor, Jeremy F.
Lewin, Harris A.
Liu, George E.
author_role author
author2 Xu, Lingyang
Hutchison, Jana L.
Cole, John B.
Null, Daniel J.
Schroeder, Steven G.
Song, Jiuzhou
Garcia, Jose Fernando [UNESP]
Sonstegard, Tad S.
Van Tassell, Curtis P.
Schnabel, Robert D.
Taylor, Jeremy F.
Lewin, Harris A.
Liu, George E.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Animal Genomics and Improvement Laboratory
University of Maryland
Universidade Estadual Paulista (Unesp)
University of Missouri
University of California
dc.subject.por.fl_str_mv cattle genome
copy number variation
indicine
population sequencing
taurine
topic cattle genome
copy number variation
indicine
population sequencing
taurine
description The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future.
publishDate 2016
dc.date.none.fl_str_mv 2016-06-15
2018-12-11T17:28:48Z
2018-12-11T17:28:48Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1093/dnares/dsw013
DNA Research, v. 23, n. 3, p. 253-262, 2016.
1756-1663
1340-2838
http://hdl.handle.net/11449/178113
10.1093/dnares/dsw013
2-s2.0-84976363605
2-s2.0-84976363605.pdf
url http://dx.doi.org/10.1093/dnares/dsw013
http://hdl.handle.net/11449/178113
identifier_str_mv DNA Research, v. 23, n. 3, p. 253-262, 2016.
1756-1663
1340-2838
10.1093/dnares/dsw013
2-s2.0-84976363605
2-s2.0-84976363605.pdf
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv DNA Research
2,866
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 253-262
application/pdf
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv repositoriounesp@unesp.br
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score 15,300719

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